The best way to prevent mod problems is to make sure your mods work properly and are compatible with each other from the moment you acquire and install them.

Try to get the latest versions of your favourite mods. These often contain bug fixes. Also look for compatibility patches if you have two mods which are incompatible (Examples: FCOM if you use any combination of OOO, MMM, Franesco's, Warcry and Bob's Armoury, Unique Landscapes has a number of compatibility patches for various mods, etc).

UseTES4Edit to clean and check your mods (only if you know how plugins work). Very easy instructions for cleaning plugins using TES4Edit are found here.

If problems start occuring right after you install a new mod, deactivate it and see if the game still causes problems. Is it for this reasont that you should only install a few mods at a time then test your game between each addition.

Remove problematic mods.

Defragment your hard drive, especially after installing a large mod. MyDefrag is probably the best free defragmenter available.